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<title>CCAnnotation.pm - A class from which all annotations used with coloredChromosomes.pl are to be derived</title>
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	<li><a href="#name">NAME</a></li>
	<li><a href="#synopsis">SYNOPSIS</a></li>
	<li><a href="#description">DESCRIPTION</a></li>
	<li><a href="#see_also">SEE ALSO</a></li>
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<h1><a name="name">NAME</a></h1>
<p>CCAnnotation.pm - A class from which all annotations used with coloredChromosomes.pl are to be derived</p>
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<h1><a name="synopsis">SYNOPSIS</a></h1>
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 Subclass by:
 @ISA = qw(CCAnnotation);
 use CCAnnotation;</pre>
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<h1><a name="description">DESCRIPTION</a></h1>
<p>This class is an abstract superclass from which all classes implementing annotations for <em>coloredChromosomes.pl</em> are derived. Each subclass has to implement the method <em>draw</em> which is to draw a single chromosome. Each instance of CCAnnotation (or a subclass) can assume that an instance variable called 'ps' is initialized. This is a Postscript object which supports many postscript operators (see <strong>Postscript</strong>). When <em>draw</em> is called the instance may safely assume the shape of the current chromosome to be the chromosomal shape, which is clipped to if the annotation is internal.</p>
<p>The following methods can be used to determine positions along the chromosome:</p>
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<code>positionFromSpec($spec)</code> - return the a relative positions (0 to 1) of the position <em>$spec</em> along the chromosome
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absolutePositionFromSpec - return the vertical position in points of the specified position
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<code>absoluteSizeOfBand($bandName)</code> - return the size of a band from the current chromosome in points
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<code>midBandPosition($bandName)</code> - return the vertical middle position of the band from the current chromosome named <em>$bandName</em> in points.
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<p>The format of specifications for chromosomal locations is detailed in the man page of <strong>coloredChromosomes.pl</strong>. The implemented annotation classes can be referred on as examples on how to explore the use of these methods.</p>
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<h1><a name="see_also">SEE ALSO</a></h1>
<p>coloredChromosomes.pl(1) <code>Postscript(3)</code></p>

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